cogent3.core.alignment.Aligned#

class Aligned(data: AlignedDataViewABC, moltype: c3_moltype.MolType[str], name: str | None = None, annotation_db: AnnotationDbABC | list[AnnotationDbABC] | None = None)#

A single sequence in an alignment.

Attributes:

annotation_db: the annotation database for the collection
data
gapped_seq: Returns Sequence object, including gaps.
map
moltype
name
seq: the ungapped sequence.

Methods

`annotate_matches_to`(pattern, biotype, name)	Adds an annotation at sequence positions matching pattern.
`from_map_and_aligned_data_view`(indel_map, seq)	Creates an Aligned instance from an indel map and AlignedDataView.
`from_map_and_seq`(indel_map, seq)	Creates an Aligned instance from an indel map and a Sequence.
`gap_vector`()	Returns gap_vector of positions.
`make_feature`(feature, alignment)	returns a feature, not written into annotation_db
`parent_coordinates`([seq_coords, apply_offset])	returns seqid, start, stop, strand on the parent sequence
`replace_annotation_db`(value[, check])	public interface to assigning the annotation_db

slice_with_map

Notes

This is a wrapper around a AlignedDataView. This class performs any complementing needed. It can be cast directly to a string or numpy array, e.g. numpy.array(<aligned instance>) returns a numpy unsigned 8-bit integer array.